The algorithm is the following: in update.f first we calculate conservative from primitive variables, then we reconstruct the conservative variables. Now we obtain the flux (again calling getflux.f) from the conservatives. Inside getflux the drill is the following: first we get primitive left and rights from conservative left and rights, we average the primitives, perform the spectral decomposition using these averaged primitives we got, obtain conservatives from the reconstructed left and right primitives, and we calculate the flux components and perform the Roe approximation. We pass control back to update.f and do our updates in fluxes and sources.
We observe similar behavior in these evolutions. In model C the unphysical transitories seems to be minimal.